Just bought an FJ40. Picking it up tomorrow. Needs some light wrenching, then it's my new daily and my wife's when she feels like it since I work out of the house and don't drive too often. Rock stock, missing only the OEM hubcaps as far as I can tell (there are a few parts in boxes that will need to be sorted, but it looks like it's all there), and the rust is very light compared to all of the others I looked at. Pretty stoked.

Boulder Toyota is cool, they have sold me TONS of FJ40 parts. I usually go there first. Non OEM can be sourced from places like NAPA for certain things like Matt says. Then for others you've got the MAF, SOR, CCOT, bunch as others have mentioned. I try to avoid SOR due to their high prices on shipping and parts. MAF and CCOT have their own demons as well, but when it comes down to it they usually have what you need and are cruiser people. I haven't tried Crusier Corps but probably will.

Used parts are the variety of FJ40 Junkyards around. Salida Classic Cruisers, cruiser parts.net All the used places you'll have to be careful about what you think you are getting. remember these things are old and most used parts will be as old and rusty as what you are trying to replace.